Hybridization detection using phylogenetic invariants
Project description
HyDe: hybridization detection using phylogenetic invariants
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Installation
Requirements:
Python 2.7
Cython
Numpy
Scipy
Pandas
Matplotlib
Seaborn
C++ compiler (g++ >= v4.8)
HyDe is a software package that detects hybridization in phylogenomic data sets using phylogenetic invariants. The primary interface for HyDe is a Python module called phyde (Pythonic Hybridization Detection). phyde provides a suite of tools for performing hypothesis tests on triples of taxa to detect hybridization. It also has built in functions to wrap calls to the pure C++ version of HyDe, hyde_cpp. We have provided a Makefile that will compile the hyde_cpp C++ executable and will then install the phyde Python package using the setup.py file. To ensure that the necessary dependencies are available, we suggest using a Python distribution such as Miniconda.
# To install dependencies
pip install cython numpy scipy pandas matplotlib seaborn
# Clone HyDe repository from GitHub
git clone https://github.com/pblischak/HyDe.git
cd HyDe
# Compile hyde_cpp using `make`
make
# Now install phyde module
python setup.py install
# Test the installation
make test
The phyde module is also hosted on the Python Package Index (PyPI), and can be installed directly using pip.
# Install from PyPI with pip
pip install phyde
Running HyDe from the Command Line
Type run_hyde.py -h for options.
run_hyde.py -i <infile> -m <map-file> -o <outgroup> \
-n <num-ind> -t <num-taxa> -s <num-sites> \
--prefix <prefix>
Running HyDe in Python
import phyde as hd
# Run a hyde analysis
res = hd.run_hyde("data.txt", "map.txt", "out", 16, 4, 50000, bootReps=100)
# import a data set for testing particular triples
data = hd.HydeData("data.txt", "map.txt", "out", 16, 4, 50000)
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